A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
/home/runner/work/pmultiqc/pmultiqc/data
pmultiqc
pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant, and DIA-NN.URL: https://github.com/bigbio/pmultiqc
Experimental Design and Metadata
Parameters
| No. | Parameter | Value |
|---|---|---|
| 1 | Version | 1.5.2.8 |
| 2 | User name | cbielow |
| 3 | Machine name | CD02-WIN7 |
| 4 | Date of writing | 08/05/2015 11:38:59 |
| 5 | Fixed modifications | Carbamidomethyl (C) |
| 6 | Decoy mode | revert |
| 7 | Special AAs | KR |
| 8 | Include contaminants | True |
| 9 | MS/MS tol. (FTMS) | 20 ppm |
| 10 | Top MS/MS peaks per 100 Da. (FTMS) | 12 |
| 11 | MS/MS deisotoping (FTMS) | True |
| 12 | MS/MS tol. (ITMS) | 0.5 Da |
| 13 | Top MS/MS peaks per 100 Da. (ITMS) | 8 |
| 14 | MS/MS deisotoping (ITMS) | False |
| 15 | MS/MS tol. (TOF) | 40 ppm |
| 16 | Top MS/MS peaks per 100 Da. (TOF) | 10 |
| 17 | MS/MS deisotoping (TOF) | True |
| 18 | MS/MS tol. (Unknown) | 0.5 Da |
| 19 | Top MS/MS peaks per 100 Da. (Unknown) | 8 |
| 20 | MS/MS deisotoping (Unknown) | False |
| 21 | PSM FDR | 0.0 |
| 22 | Protein FDR | 0.0 |
| 23 | Site FDR | 0.0 |
| 24 | Use Normalized Ratios For Occupancy | True |
| 25 | Min. peptide Length | 7 |
| 26 | Min. score for unmodified peptides | 0 |
| 27 | Min. score for modified peptides | 40 |
| 28 | Min. delta score for unmodified peptides | 0 |
| 29 | Min. delta score for modified peptides | 6 |
| 30 | Min. unique peptides | 0 |
| 31 | Min. razor peptides | 1 |
| 32 | Min. peptides | 1 |
| 33 | Use only unmodified peptides and | True |
| 34 | Modifications included in protein quantification | Acetyl (Protein N-term);Oxidation (M) |
| 35 | Peptides used for protein quantification | Razor |
| 36 | Discard unmodified counterpart peptides | True |
| 37 | Min. ratio count | 2 |
| 38 | Re-quantify | False |
| 39 | Use delta score | False |
| 40 | iBAQ | False |
| 41 | iBAQ log fit | False |
| 42 | Match between runs | True |
| 43 | Matching time window [min] | 0.7 |
| 44 | Alignment time window [min] | 20 |
| 45 | Find dependent peptides | False |
| 46 | Fasta file | crap_withMycoplasma.fasta;uniprot_human_canonical_and_isoforms_20130513.fasta |
| 47 | Labeled amino acid filtering | True |
| 48 | Site tables | Oxidation (M)Sites.txt |
| 49 | RT shift | False |
| 50 | Advanced ratios | True |
| 51 | First pass AIF correlation | 0.8 |
Results Overview
Summary Table
| #MS2 Spectra | #Identified MS2 Spectra | %Identified MS2 Spectra | #Peptides Identified | #Proteins Identified | #Proteins Quantified |
|---|---|---|---|---|---|
| 201567 | 84900 | 42.12% | 28949 | 4053 | 4048 |
HeatMap
Identification Summary
Number of Peptides identified Per Protein
ProteinGroups Count [MBR gain: +8.8%]
Peptide ID Count [MBR gain: +18.46%]
Missed Cleavages Per Raw File
Modifications Per Raw File
MS/MS Identified Per Raw File
Search Engine Scores
Summary of Andromeda Scores
Contaminants
Top5 Contaminants Per Raw File
Potential Contaminants Per File
Quantification Analysis
Intensity Distribution
LFQ Intensity Distribution
Peptide Intensity Distribution
PCA of Raw Intensity
PCA of LFQ Intensity
Peptides Quantification Table
| PeptideID | Protein Name | Peptide Sequence | Best Search Score | Average Intensity |
|---|---|---|---|---|
| 1 | Q86U42-2;Q86U42 | AAAAAAAAAAGAAGGR | 128.6800 | 7.1389 |
| 2 | P37108 | AAAAAAAAAPAAAATAPTTAATTAATAAQ | 82.8310 | 7.1284 |
| 3 | P36578 | AAAAAAALQAK | 135.4300 | 7.8269 |
| 4 | Q9H3H3-2;Q9H3H3-3 | AAAAAAAVAGVGR | 108.3100 | 6.4210 |
| 5 | Q96P70 | AAAAAAGAASGLPGPVAQGLK | 85.9370 | 6.6024 |
| 6 | P28482 | AAAAAAGAGPEMVR | 94.1220 | 6.4680 |
| 7 | Q8WVM8 | AAAAAATAAAAASIR | 146.5900 | 6.6441 |
| 8 | Q86X55-1;Q86X55;Q86X55-2 | AAAAAAVGPGAGGAGSAVPGGAGPCATVSVFPGAR | 59.5360 | 6.6710 |
| 9 | O00410 | AAAAAEQQQFYLLLGNLLSPDNVVR | 99.1100 | 6.7391 |
| 10 | O00410 | AAAAAEQQQFYLLLGNLLSPDNVVRK | 74.7030 | 6.7286 |
| 11 | P86791;P86790 | AAAAAGAGSGPWAAQEK | 82.9420 | 6.2996 |
| 12 | Q9Y2Z0-2;Q9Y2Z0 | AAAAAGTATSQR | 124.4200 | 7.5048 |
| 13 | Q7L5D6 | AAAAAMAEQESAR | 117.0300 | 6.0297 |
| 14 | Q13049 | AAAAASHLNLDALR | 88.7060 | 6.3835 |
| 15 | Q9P258 | AAAAAWEEPSSGNGTAR | 137.2700 | 6.1486 |
| 16 | O43324-2;O43324 | AAAAELSLLEK | 169.5200 | 6.9630 |
| 17 | Q96KQ7-2;Q96KQ7;Q96KQ7-3 | AAAAGAAAAAAAEGEAPAEMGALLLEK | 89.4620 | 5.9631 |
| 18 | Q00796 | AAAAKPNNLSLVVHGPGDLR | 112.8200 | 7.1325 |
| 19 | P55036 | AAAASAAEAGIATTGTEDSDDALLK | 54.0470 | 6.4029 |
| 20 | Q15005 | AAAAVQGGR | 127.4600 | 6.8615 |
| 21 | Q8N1G4 | AAAAVSESWPELELAER | 104.2100 | 6.1032 |
| 22 | O00231;O00231-2 | AAAAVVEFQR | 105.9800 | 6.9886 |
| 23 | Q8NI27 | AAAAVVVPAEWIK | 59.2270 | 6.5836 |
| 24 | P30153 | AAADGDDSLYPIAVLIDELR | 85.2030 | 6.1322 |
| 25 | Q9UNF1-2;Q9UNF1 | AAAEAAAEAK | 91.7010 | 5.2648 |
| 26 | Q9NQP4 | AAAEDVNVTFEDQQK | 147.7500 | 5.9965 |
| 27 | P55263;P55263-3 | AAAEEEPKPK | 86.8980 | 6.2054 |
| 28 | Q99567 | AAAEGPVGDGELWQTWLPNHVVFLR | 80.2360 | 6.2906 |
| 29 | Q13523 | AAAETQSLR | 76.1700 | 6.4857 |
| 30 | P02786 | AAAEVAGQFVIK | 117.2000 | 6.6548 |
| 31 | Q9Y490 | AAAFEEQENETVVVK | 130.4700 | 6.2308 |
| 32 | O94826 | AAAFEQLQK | 78.5560 | 6.9091 |
| 33 | P35221;P35221-2 | AAAGEFADDPCSSVK | 120.2100 | 6.7622 |
| 34 | Q96C19 | AAAGELQEDSGLCVLAR | 170.4700 | 6.5967 |
| 35 | Q9UL25 | AAAGGGGGGAAAAGR | 182.7100 | 6.7549 |
| 36 | Q96T51;Q96T51-3 | AAAGLGGGDSGDGTAR | 108.6600 | 6.6020 |
| 37 | P51970 | AAAHHYGAQCDKPNK | 44.4360 | 5.2035 |
| 38 | P08107;P08107-2 | AAAIGIDLGTTYSCVGVFQHGK | 60.0620 | 6.7559 |
| 39 | Q14008-2;Q14008;Q14008-3 | AAALATVNAWAEQTGMK | 172.4200 | 6.1280 |
| 40 | P31948 | AAALEFLNR | 82.2870 | 6.3951 |
| 41 | P31948 | AAALEFLNRFEEAK | 137.8100 | 7.3349 |
| 42 | O60716-13;O60716-11;O60716-10;O60716-9;O60716-21;O60716-19;O60716-16;O60716-18;O60716-15;O60716-17;O60716-14;O60716-12;O60716-5;O60716-3;O60716-2;O60716;O60716-24;O60716-23;O60716-22;O60716-20;O60716-8;O60716-7;O60716-6;O60716-4;O60716-29;O60716-27;O60716-26;O60716-25;O60716-32;O60716-31;O60716-30;O60716-28 | AAALVLQTIWGYK | 145.8100 | 6.3166 |
| 43 | Q14498-2;Q14498;Q14498-3 | AAAMANNLQK | 73.2330 | 5.4044 |
| 44 | P62877 | AAAMDVDTPSGTNSGAGK | 168.4200 | 5.9619 |
| 45 | P62877 | AAAMDVDTPSGTNSGAGKK | 186.7200 | 6.6983 |
| 46 | Q9NX63 | AAANEQLTR | 107.4500 | 6.4553 |
| 47 | P26641 | AAAPAPEEEMDECEQALAAEPK | 131.5600 | 6.6380 |
| 48 | P20810-7;P20810-6;P20810-5;P20810-4;P20810-8;P20810;P20810-2;P20810-3 | AAAPAPVSEAVCR | 90.7930 | 7.3560 |
| 49 | Q12765 | AAAPPSYCFVAFPPR | 56.5690 | 5.7088 |
| 50 | P53618 | AAAQCYIDLIIK | 77.6440 | 6.8017 |
Protein Quantification Table
| ProteinID | Protein Name | Number of Peptides | Average Intensity |
|---|---|---|---|
| 1 | A0AV96-2;A0AV96 | 2 | 5.8834 |
| 2 | A0AVT1 | 1 | 6.9224 |
| 3 | A0AVT1;A0AVT1-2 | 19 | 6.4333 |
| 4 | A0AVT1;A0AVT1-3 | 1 | 6.0380 |
| 5 | A0AVT1;A0AVT1-3;A0AVT1-4 | 6 | 6.3704 |
| 6 | A0FGR8-2 | 1 | 5.4654 |
| 7 | A0FGR8-2;A0FGR8;A0FGR8-6 | 1 | 5.5375 |
| 8 | A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-4 | 6 | 6.5283 |
| 9 | A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-4;A0FGR8-5 | 1 | 6.6685 |
| 10 | A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 | 4 | 6.4869 |
| 11 | A0MZ66-2;A0MZ66-8;A0MZ66-4;A0MZ66-5;A0MZ66-6;A0MZ66;A0MZ66-3 | 2 | 6.2240 |
| 12 | A1L0T0 | 12 | 6.3070 |
| 13 | A2RRP1-2;A2RRP1 | 3 | 5.7738 |
| 14 | A4D1E9 | 1 | 5.7467 |
| 15 | A4D1E9;A4D1E9-2 | 1 | 6.2192 |
| 16 | A4UGR9-2;A4UGR9-3;A4UGR9 | 1 | 6.4718 |
| 17 | A5D8W1-2;A5D8W1-5;A5D8W1 | 1 | 6.5837 |
| 18 | A5D8W1-2;A5D8W1-5;A5D8W1;A5D8W1-4;A5D8W1-3 | 1 | 6.5649 |
| 19 | A5YKK6-2;A5YKK6 | 1 | 6.1066 |
| 20 | A5YKK6-2;A5YKK6;A5YKK6-3 | 4 | 5.8559 |
| 21 | A5YKK6-2;A5YKK6;A5YKK6-3;A5YKK6-4 | 4 | 6.0792 |
| 22 | A6NDG6 | 4 | 6.1718 |
| 23 | A6NDU8 | 1 | 6.1976 |
| 24 | A6NFZ4 | 1 | 5.3669 |
| 25 | A6NHL2-2;A6NHL2 | 1 | 6.6717 |
| 26 | A6NHQ2 | 1 | 6.9258 |
| 27 | A6NHR9 | 1 | 6.3482 |
| 28 | A6NHR9;A6NHR9-2 | 9 | 6.1953 |
| 29 | A6NHR9;A6NHR9-2;A6NHR9-3 | 6 | 6.3258 |
| 30 | A6NKF9;B7ZAQ6-2;B7ZAQ6-3;P0CG08;B7ZAQ6 | 1 | 5.9271 |
| 31 | A6NKT7;Q7Z3J3 | 1 | 5.9068 |
| 32 | A6NKT7;Q7Z3J3;P0DJD0;P0DJD1;Q8IWJ2 | 1 | 5.6636 |
| 33 | A8MT69 | 1 | 5.4836 |
| 34 | A8MXV4 | 3 | 6.2205 |
| 35 | C9JLW8 | 1 | 6.1450 |
| 36 | CONTAMINANT_sp|ANXA5_HUMAN|;P08758 | 25 | 7.4325 |
| 37 | CONTAMINANT_sp|B2MG_HUMAN|;P61769 | 3 | 7.6794 |
| 38 | CONTAMINANT_sp|BID_HUMAN|;P55957;P55957-2 | 1 | 5.7736 |
| 39 | CONTAMINANT_sp|BID_HUMAN|;P55957;P55957-2;P55957-3 | 1 | 6.5969 |
| 40 | CONTAMINANT_sp|BID_HUMAN|;P55957;P55957-2;P55957-4 | 4 | 6.2732 |
| 41 | CONTAMINANT_sp|CATA_HUMAN|;P04040 | 13 | 6.7989 |
| 42 | CONTAMINANT_sp|CATD_HUMAN|;P07339 | 21 | 7.2581 |
| 43 | CONTAMINANT_sp|CYC_HUMAN|;P99999 | 5 | 6.9857 |
| 44 | CONTAMINANT_sp|CYC_HUMAN|;P99999;CONTAMINANT_sp|CYC_HORSE|;CON__P62894 | 2 | 7.0820 |
| 45 | CONTAMINANT_sp|NEDD8_HUMAN|;Q15843 | 2 | 6.6189 |
| 46 | CONTAMINANT_sp|NQO2_HUMAN|;P16083 | 2 | 6.4140 |
| 47 | CONTAMINANT_sp|PRDX1_HUMAN|;Q06830 | 12 | 7.8054 |
| 48 | CONTAMINANT_sp|PRDX1_HUMAN|;Q06830;P32119 | 1 | 8.0652 |
| 49 | CONTAMINANT_sp|PRDX1_HUMAN|;Q06830;Q13162 | 2 | 7.8547 |
| 50 | CONTAMINANT_sp|RS27A_HUMAN|;P62979 | 2 | 7.2087 |